According to the ABC, some Australian staff took cover alongside detainees inside the facility, while others were seen running for a boat moored nearby.

In a statement to Guardian Australia, the department said an “incident” had occurred at the detention centre, involving residents and PNG military personnel.

It said there were reports that PNG military personnel had “discharged a weapon into the air”, but no one was injured by gunfire.

One “resident” had been hurt by a thrown rock and was receiving treatment, the department said; all other detainees were safe.

But Behrouz Boochani, an Iranian-born journalist and asylum seeker held on Manus Island, told Guardian Australia that three refugees – two from Sudan, and one from Pakistan – and some Australian guards had been seriously injured by stones thrown in the attack.

Some of the officers were beaten “very seriously”, said Boochani.

Guardian Australia has put this to the department and is awaiting a response.

Boochani was tweeting from the compound as the situation unfolded late on Friday. “The situation on Manus is critical,” he wrote.

Later, about 10.30pm, he tweeted that the Australian staff unexpectedly left the centre, leaving the detainees unprotected for about half an hour.

Boochani’s report that more than 100 shots were fired was confirmed by the Refugee Action Coalition. He disputed the department’s account that the navy had fired guns into the air, pointing to footage showing bullet holes in fences and walls.

“Last night police were around the centre all night to protect the refugees and Australian staff. On the other side of the fences, in staff accommodation, the Australian non-security staff like case managers, interpreters, and immigration were scared too. I talked with some of them and they were in an unsafe place like the refugees. Some of those staff did not come to work today. Last night proved that Australia cannot ensure safety not only for refugees but for its citizens too.”

Shayne Neumann, Australia’s opposition immigration spokesman, said in a news release that the incident was “concerning and must be fully investigated”.

“There have been conflicting reports about how and why this incident began and the types of force used by authorities on Manus Island. The culture of secrecy must change.”

Amnesty International echoed the calls for an investigation into the “shocking shooting incident”, adding that it was further evidence the Manus detention facility was not a safe place for asylum seekers.

Anna Neistat, the group’s senior research director, said further incidents were “inevitable” if refugees and asylum seekers were not relocated to safety.

In February 2014, the Iranian asylum seeker Reza Barati was killed and more than 70 others seriously injured in an attack on centre by local security guards and residents.

Daniel Webb, the legal advocacy director at the Human Rights Law Centre, compared those riots three years ago to the “terrifying and violent attack” on Friday night.

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“Most of these men were found to be refugees years ago. Last night’s attack has again left them terrified and – after four years of fear, violence and limbo – they are completely exhausted.

“I first visited the camp just after Reza Barati’s murder in 2014 and I saw how terrified and tired the men were back then. Yet more than three years later those men are still trapped behind the same fence and living in constant fear. Last night they were once again hiding in their rooms from outsiders intent on attacking them.

“This can’t go on another day.”

Webb said the lives of the men were in the hands of the prime minister, Malcolm Turnbull. “These attacks show just how urgent the situation is.”

The Manus Island detention centre is due to close on 31 October.

The immigration minister, Peter Dutton, has said that those refugees who are not taken under an agreement with the US will be settled in Papua New Guinea, while non-refugees will be sent back to their home country.

People now detained on Manus Island will not be coming to Australia, no matter how hard refugee advocates push, Dutton said this week.